One possible plot twist could be that Naruto's unique way of raising the Sannin changes their personalities completely. For example, Jiraiya might become more reserved and studious under Naruto's influence. Another could be that the Sannin end up teaching Naruto secrets that were lost in the original timeline. Maybe Tsunade reveals a new form of medical ninjutsu that Naruto then uses to save many lives in future battles. Also, Orochimaru might turn away from his dark path earlier, leading to a different power structure in the shinobi world.
Well, a major plot twist in a 'Naruto Raised Sannin Fanfic' could be that Naruto, in the process of raising the Sannin, discovers a hidden prophecy about them. This prophecy could state that they are the key to a new form of chakra that could either save or destroy the ninja world. So, Naruto has to be extra careful with how he guides them. And, it's possible that the Sannin develop a new team jutsu together, which they then use to fend off a much greater threat than in the original story, like an alien invasion of sorts (yes, that's a bit far - fetched but it's fanfic so anything goes).
Naruto would likely be more confident. With the Sannin as his guardians, he'd have access to top - notch training and knowledge. He might not have the same insecurities as in the original series. For example, Tsunade could help him with his self - esteem, Jiraiya with his understanding of the ninja world, and Orochimaru (in a reformed way) with his knowledge of forbidden jutsu, making him a more well - rounded and confident shinobi.
One possible plot twist could be that Naruto develops unique jutsu influenced by Yugito's Nibi powers. Since Yugito is a jinchuriki, she might teach Naruto some special techniques related to chakra control and dealing with tailed beasts. For example, Naruto could learn a new form of Rasengan that incorporates some of the Nibi's chakra nature.
A really interesting plot twist could be that Zabuza has a hidden past or connection to Naruto's family. For instance, perhaps he knew Naruto's father in a different context than what was previously known. This could change Naruto's whole perspective on his family and his place in the ninja world. Or, Zabuza could have been given a secret mission long ago related to Naruto that he never fully completed, and now raising Naruto becomes a way to fulfill that mission. This would add a whole new layer of mystery and depth to the fanfic.
I think Orochimaru would be the most changed. In the original series, he was very much into dark and forbidden jutsu. But if Naruto were to raise him, Naruto's positive influence would likely steer him away from that path. He might become more of a healer or a researcher into non - harmful ninjutsu.
Well, it could be that Naruto gets super powerful training from each of the Sannin. Jiraiya might teach him more advanced toad jutsus and how to better control his chakra. Tsunade could train him in medical ninjutsu and physical combat skills. Orochimaru, even though he's a bit of a dark character, could show Naruto some really unique and forbidden jutsus that Naruto has to learn to resist the dark side of. And all this special training could make Naruto a much more formidable shinobi in the fanfic.
A plot twist could be that Naruto's Fuinjutsu skills are actually part of a prophecy in Kumo. The village initially hid this from him, but as he progresses in learning, he discovers the truth and has to deal with the implications.
A really interesting plot twist could be in the area of Naruto's chakra nature. Zetsu has some strange abilities related to plants and the earth. So, Naruto, being raised by Zetsu, might develop a new type of chakra nature that combines his own wind nature with something more related to earth or plant - like. This would make his jutsu look very different. For example, his Rasengan could be infused with some kind of plant - based energy that not only causes damage but also has some sort of healing or growth - promoting effect on the surrounding area. And his relationships with other characters would be different too. Since he's been raised by Zetsu, he might be more of an enigma to his peers in the Hidden Leaf Village, and they might be more suspicious of him.
One possible plot twist could be that Naruto develops Uchiha - like abilities early on. Since the Uchiha are known for their Sharingan and powerful fire - style jutsu, Naruto might accidentally awaken a form of Sharingan - like power due to being raised in an Uchiha - influenced environment. This could cause a stir in the ninja world as it goes against the normal development of a Jinchuriki.
One possible plot twist could be that Naruto's ninja skills are enhanced in a unique way due to Aphrodite's influence. Maybe his charm becomes a weapon, like he can disarm opponents just by using his new - found allure. Another could be that Naruto has to face the wrath of other gods who don't like Aphrodite interfering in the mortal world in this way.
One interesting plot twist could be that the Sannin travel back to a time when Orochimaru was still a good - hearted ninja. They could try to prevent his fall to the dark side. This would change the entire future of the Naruto world as Orochimaru's actions had a huge impact on many events.